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Obenauer ML, Dresel JA, Schweitzer M, Besenius P, Schmid F. Atomistic Molecular Dynamics Simulations of ABA-Type Polymer Peptide Conjugates: Insights into Supramolecular Structures and their Circular Dichroism Spectra. Macromol Rapid Commun 2024:e2400149. [PMID: 38973657 DOI: 10.1002/marc.202400149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 06/16/2024] [Indexed: 07/09/2024]
Abstract
A combination of atomistic molecular dynamics (aMD) simulations and circular dichroism (CD) analysis is used to explore supramolecular structures of amphiphilic ABA-type triblock polymer peptide conjugates (PPC). Using the example of a recently introduced PPC with pH- and temperature responsive self-assembling behavior [Otter et al., Macromolecular Rapid Communications 2018, 39, 1800459], this study shows how molecular dynamics simulations of simplified fragment molecules can add crucial information to CD data, which helps to correctly identify the self-assembled structures and monitor the folding/unfolding pathways of the molecules. The findings offer insights into the nature of structural transitions induced by external stimuli, thus contributing to the understanding of the connection of microscopic structures with macroscopic properties.
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Affiliation(s)
| | | | - Maren Schweitzer
- Department of Chemistry, Duesbergweg 10-14, D-55128, Mainz, Germany
| | - Pol Besenius
- Department of Chemistry, Duesbergweg 10-14, D-55128, Mainz, Germany
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Wu Z, Wu JW, Michaudel Q, Jayaraman A. Investigating the Hydrogen Bond-Induced Self-Assembly of Polysulfamides Using Molecular Simulations and Experiments. Macromolecules 2023; 56:5033-5049. [PMID: 38362140 PMCID: PMC10865372 DOI: 10.1021/acs.macromol.3c01093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 06/08/2023] [Indexed: 02/17/2024]
Abstract
In this paper, we present a synergistic, experimental, and computational study of the self-assembly of N,N'-disubstituted polysulfamides driven by hydrogen bonds (H-bonds) between the H-bonding donor and acceptor groups present in repeating sulfamides as a function of the structural design of the polysulfamide backbone. We developed a coarse-grained (CG) polysulfamide model that captures the directionality of H-bonds between the sulfamide groups and used this model in molecular dynamics (MD) simulations to study the self-assembly of these polymers in implicit solvent. The CGMD approach was validated by reproducing experimentally observed trends in the extent of crystallinity for three polysulfamides synthesized with aliphatic and/or aromatic repeating units. After validation of our CGMD approach, we computationally predicted the effect of repeat unit bulkiness, length, and uniformity of segment lengths in the polymers on the extent of orientational and positional order among the self-assembled polysulfamide chains, providing key design principles for tuning the extent of crystallinity in polysulfamides in experiments. Those computational predictions were then experimentally tested through the synthesis and characterization of polysulfamide architectures.
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Affiliation(s)
- Zijie Wu
- Department
of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy St., Newark, Delaware 19716, United States
| | - Jiun Wei Wu
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Quentin Michaudel
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Materials Science & Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Arthi Jayaraman
- Department
of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy St., Newark, Delaware 19716, United States
- Department
of Materials Science and Engineering, University
of Delaware, 201 DuPont Hall, Newark, Delaware 19716, United States
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3
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Liang H, Webb MA, Chawathe M, Bendejacq D, de Pablo JJ. Understanding the Structure and Rheology of Galactomannan Solutions with Coarse-Grained Modeling. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c01781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Heyi Liang
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois60637, United States
| | - Michael A. Webb
- Chemical and Biological Engineering, Princeton University, Princeton, New Jersey08544, United States
| | - Manasi Chawathe
- Complex Assemblies of Soft Matter Laboratory, IRL 3254, Solvay USA Inc., Bristol, Pennsylvania19007, United States
| | - Denis Bendejacq
- Complex Assemblies of Soft Matter Laboratory, IRL 3254, Solvay USA Inc., Bristol, Pennsylvania19007, United States
| | - Juan J. de Pablo
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois60637, United States
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Abstract
Glycoscience assembles all the scientific disciplines involved in studying various molecules and macromolecules containing carbohydrates and complex glycans. Such an ensemble involves one of the most extensive sets of molecules in quantity and occurrence since they occur in all microorganisms and higher organisms. Once the compositions and sequences of these molecules are established, the determination of their three-dimensional structural and dynamical features is a step toward understanding the molecular basis underlying their properties and functions. The range of the relevant computational methods capable of addressing such issues is anchored by the specificity of stereoelectronic effects from quantum chemistry to mesoscale modeling throughout molecular dynamics and mechanics and coarse-grained and docking calculations. The Review leads the reader through the detailed presentations of the applications of computational modeling. The illustrations cover carbohydrate-carbohydrate interactions, glycolipids, and N- and O-linked glycans, emphasizing their role in SARS-CoV-2. The presentation continues with the structure of polysaccharides in solution and solid-state and lipopolysaccharides in membranes. The full range of protein-carbohydrate interactions is presented, as exemplified by carbohydrate-active enzymes, transporters, lectins, antibodies, and glycosaminoglycan binding proteins. A final section features a list of 150 tools and databases to help address the many issues of structural glycobioinformatics.
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Affiliation(s)
- Serge Perez
- Centre de Recherche sur les Macromolecules Vegetales, University of Grenoble-Alpes, Centre National de la Recherche Scientifique, Grenoble F-38041, France
| | - Olga Makshakova
- FRC Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, Kazan 420111, Russia
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Ramamohan P, Furó I, Wohlert J. Timescales for convergence in all-atom molecular dynamics simulations of hydrated amorphous xylan. Carbohydr Polym 2022; 286:119263. [DOI: 10.1016/j.carbpol.2022.119263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 02/04/2022] [Accepted: 02/15/2022] [Indexed: 11/02/2022]
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Dhamankar S, Webb MA. Chemically specific coarse‐graining of polymers: Methods and prospects. JOURNAL OF POLYMER SCIENCE 2021. [DOI: 10.1002/pol.20210555] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Satyen Dhamankar
- Department of Chemical and Biological Engineering Princeton University Princeton New Jersey USA
| | - Michael A. Webb
- Department of Chemical and Biological Engineering Princeton University Princeton New Jersey USA
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Abstract
Cellulose is the most common biopolymer and widely used in our daily life. Due to its unique properties and biodegradability, it has been attracting increased attention in the recent years and various new applications of cellulose and its derivatives are constantly being found. The development of new materials with improved properties, however, is not always an easy task, and theoretical models and computer simulations can often help in this process. In this review, we give an overview of different coarse-grained models of cellulose and their applications to various systems. Various coarse-grained models with different mapping schemes are presented, which can efficiently simulate systems from the single cellulose fibril/crystal to the assembly of many fibrils/crystals. We also discuss relevant applications of these models with a focus on the mechanical properties, self-assembly, chiral nematic phases, conversion between cellulose allomorphs, composite materials and interactions with other molecules.
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Lu S, Wu Z, Jayaraman A. Molecular Modeling and Simulation of Polymer Nanocomposites with Nanorod Fillers. J Phys Chem B 2021; 125:2435-2449. [PMID: 33646794 DOI: 10.1021/acs.jpcb.1c00097] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We present a coarse-grained (CG) molecular dynamics (MD) simulation study of polymer nanocomposites (PNCs) containing nanorods with homogeneous and patchy surface chemistry/functionalization, modeled with isotropic and directional nanorod-nanorod attraction, respectively. We show how the PNC morphology is impacted by the nanorod design (i.e., aspect ratio, homogeneous or patchy surface chemistry/functionalization) for nanorods with a diameter equal to the Kuhn length of the polymer in the matrix. For PNCs with 10 vol % nanorods that have an aspect ratio ≤5, we observe percolated morphology with directional nanorod-nanorod attraction and phase-separated (i.e., nanorod aggregation) morphology with isotropic nanorod-nanorod attraction. In contrast, for nanorods with higher aspect ratios, both types of attractions result in aggregated nanorods morphology due to the dominance of entropic driving forces that cause long nanorods to form orientationally ordered aggregates. For most PNCs with isotropic or directional nanorod-nanorod attractions, the average matrix polymer conformation is not perturbed by the inclusion of up to 20 vol % nanorods. The polymer chains in contact with nanorods (i.e., interfacial chains) are on average extended and statistically different from the conformations the matrix chains adopt in the pure melt state (with no nanorods); in contrast, the polymer chains far from nanorods (i.e., bulk chains) adopt the same conformations as the matrix chains adopt in the pure melt state. We also study the effect of other parameters, such as attraction strength, nanorod volume fraction, and matrix chain length, for PNCs with isotropic or directional nanorod-nanorod attractions. Collectively, our results provide valuable design rules to achieve specific PNC morphologies (i.e., dispersed, aggregated, percolated, and orientationally aligned nanorods) for various potential applications.
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Affiliation(s)
- Shizhao Lu
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States
| | - Zijie Wu
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States
| | - Arthi Jayaraman
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States.,Department of Materials Science and Engineering, University of Delaware, 201 DuPont Hall, Newark, Delaware 19716, United States
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Souza FR, Souza LMP, Pimentel AS. Recent Open Issues in Coarse Grained Force Fields. J Chem Inf Model 2020; 60:5881-5884. [PMID: 33231448 DOI: 10.1021/acs.jcim.0c01265] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This viewpoint intends to show recent open issues of using coarse grained models in molecular dynamics simulation. It reviews the current knowledge of the comparison between experimental and simulation data of structural and physical chemical properties that depend on the hydrophilic and hydrophobic behavior of the molecule.
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Affiliation(s)
- Felipe Rodrigues Souza
- Departamento de Química, Pontifícia Universidade Católica do Rio de Janeiro, Rio de Janeiro, RJ 22453-900 Brazil
| | - Lucas Miguel Pereira Souza
- Departamento de Química, Pontifícia Universidade Católica do Rio de Janeiro, Rio de Janeiro, RJ 22453-900 Brazil
| | - Andre Silva Pimentel
- Departamento de Química, Pontifícia Universidade Católica do Rio de Janeiro, Rio de Janeiro, RJ 22453-900 Brazil
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Taylor PA, Huang H, Kiick KL, Jayaraman A. Placement of Tyrosine Residues as a Design Element for Tuning the Phase Transition of Elastin-peptide-containing Conjugates: Experiments and Simulations. MOLECULAR SYSTEMS DESIGN & ENGINEERING 2020; 5:1239-1254. [PMID: 33796336 PMCID: PMC8009313 DOI: 10.1039/d0me00051e] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Elastin-like polypeptides (ELP) have been widely used in the biomaterials community due to their controllable, thermoresponsive properties and biocompatibility. Motivated by our previous work on the effect of tryptophan (W) substitutions on the LCST-like transitions of short ELPs, we studied a series of short ELPs containing tyrosine (Y) and/or phenylalanine (F) guest residues with only 5 or 6 pentapeptide repeat units. A combination of experiments and molecular dynamics (MD) simulations illustrated that the substitution of F with Y guest residues impacted the transition temperature (Tt) of short ELPs when conjugated to collagen-like-peptides (CLP), with a reduction in the transition temperature observed only after substitution of at least two residues. Placement of the Y residues near the N-terminal end of the ELP, away from the tethering point to the CLP, resulted in a lower Tt than that observed for peptides with the Y residues near the tethering point. Atomistic and coarse-grained MD simulations indicated an increase in intra- and inter- peptide hydrogen bonds in systems containing Y guest residues that are suggested to enhance the ability of the peptides to coacervate, with a concomitantly lower Tt. Simulations also revealed that the placement of Y-containing pentads near the N-terminus (i.e., away from CLP tethering point) versus C-terminus of the ELP led to more π-π stacking interactions at low temperatures, in agreement with our experimental observations of a lower Tt. Overall, this study provides mechanistic insights into the driving forces for the LCST-like transitions of ELPs and offers additional means for tuning the Tt of short ELPs for biomedical applications such as on-demand drug delivery and tissue engineering.
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Affiliation(s)
- Phillip A. Taylor
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716 USA
| | - Haofu Huang
- Department of Materials Science and Engineering, University of Delaware, Newark, DE 19716 USA
| | - Kristi L. Kiick
- Department of Materials Science and Engineering, University of Delaware, Newark, DE 19716 USA
| | - Arthi Jayaraman
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716 USA
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Wu Z, Beltran-Villegas DJ, Jayaraman A. Development of a New Coarse-Grained Model to Simulate Assembly of Cellulose Chains Due to Hydrogen Bonding. J Chem Theory Comput 2020; 16:4599-4614. [DOI: 10.1021/acs.jctc.0c00225] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Zijie Wu
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy
St., Newark, Delaware 19716, United States
| | - Daniel J. Beltran-Villegas
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy
St., Newark, Delaware 19716, United States
| | - Arthi Jayaraman
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy
St., Newark, Delaware 19716, United States
- Department of Materials Science and Engineering, University of Delaware, 201 DuPont Hall, Newark, Delaware 19716, United States
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12
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Jayaraman A. 100th Anniversary of Macromolecular Science Viewpoint: Modeling and Simulation of Macromolecules with Hydrogen Bonds: Challenges, Successes, and Opportunities. ACS Macro Lett 2020; 9:656-665. [PMID: 35648569 DOI: 10.1021/acsmacrolett.0c00134] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Macromolecular materials with directional interactions such as hydrogen bonds exhibit numerous attractive features in terms of structure, thermodynamics, and dynamics. Besides enabling precise tuning of desirable geometries in the assembled state (e.g., programmable coordination numbers depending on the valency of the directional interaction), mixing in a blend/composite through stabilization via hydrogen bonds between the various components, hydrogen bonds can also impart responsiveness to external stimuli (e.g., temperature, pH). In biomacromolecules (e.g., proteins, DNA, polysaccharides), hydrogen bonds play a key role in stabilizing secondary and tertiary structures, which in turn define the function of these macromolecules. In this Viewpoint, I present the challenges, successes, and opportunities for molecular modeling and simulations to conduct fundamental and application-focused research on macromolecular materials with hydrogen bonding interactions. The past successes and limitations of atomistic simulations are discussed first, followed by highlights from recent developments in coarse-grained modeling and their use in studies of (synthetic and biologically relevant) macromolecular materials. Model development focused on polynucleotides (e.g., DNA, RNA, etc.), polypeptides, polysaccharides, and synthetic polymers at experimentally relevant conditions are highlighted. This viewpoint ends with potential future directions for macromolecular modeling and simulations with other types of directional interactions beyond hydrogen bonding.
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Affiliation(s)
- Arthi Jayaraman
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
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